It is the same core, but that doesn't mean that it shouldn't be handled differently. The thermal rating of the Apple's quad chip is reputed to be 150W. The standard Clovertown is 120W. Standard Woodcrest is about 75W.
I think that is just two different offerings of the exact same chip with the same ratings. I think you can buy the bare chip in bulk from Intel, or buy the retail box which generally includes a heat sink & fan. There is also a separate kit yet again for 1U computers because of the height limitation.
I question buying a such expensive computer, disassemble it and leave it disassembled for days, why spend that much and not use it days? I did take out parts of my Mac Pro, but I never touched the heat sink.